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Title

Phylogenetic reconstruction of endophytic fungal isolates using internal transcribed spacer 2 (ITS2) region 

 

Authors

Kathamuthu GokulRaj1, Natesan Sundaresan1, Enthai Jagan Ganeshan1, Pandi Rajapriya2, Johnpaul Muthumary3, Jayavel Sridhar4 & Mohan Pandi1*

 

Affiliation

1Department of Molecular Microbiology, School of Biotechnology, Madurai Kamaraj University, Madurai 21, Tamil Nadu, India; 2Department of Microbial Technology, School of Biological Sciences, Madurai Kamaraj University, Madurai 21, Tamil Nadu, India; 3Centre for Advanced Studies in Botany, University of Madras, Guindy Campus, Chennai 25, Tamil Nadu, India.; 4Department of Biotechnology (DDE), Madurai Kamaraj University, Madurai 21, Tamil Nadu, India

 

Email

an_pandi@rediffmail.com, pandimohan81@gmail.com; *Corresponding author

 

Article Type

Hypothesis

 

Date

Received May 13, 2014; Accepted May 23, 2014; Published June 30, 2014

 

Abstract

Endophytic fungi are inhabitants of plants, living most part of their lifecycle asymptomatically which mainly confer protection and ecological advantages to the host plant. In this present study, 48 endophytic fungi were isolated from the leaves of three medicinal plants and characterized based on ITS2 sequence secondary structure analysis. ITS2 secondary structures were elucidated with minimum free energy method (MFOLD version 3.1) and consensus structure of each genus was generated by 4SALE. ProfDistS was used to generate ITS2 sequence structure based phylogenetic tree respectively. Our elucidated isolates were belonging to Ascomycetes family, representing 5 orders and 6 genera. Colletotrichum/Glomerella spp., Diaporthae/Phomopsis spp., and Alternaria spp., were predominantly observed while Cochliobolus sp., Cladosporium sp., and Emericella sp., were represented by singletons. The constructed phylogenetic tree has well resolved monophyletic groups with >50% bootstrap value support. Secondary structures based fungal systematics improves not only the stability; it also increases the precision of phylogenetic inference. Above ITS2 based phylogenetic analysis was performed for our 48 isolates along with sequences of known ex-types taken from GenBank which confirms the efficiency of the proposed method. Further, we propose it as superlative marker for reconstructing phylogenetic relationships at different taxonomic levels due to their lesser length.

 

Keywords

Endophytes, ITS, MEGA 5.1, ProfDistS, Sequence-secondary structure, 4SALE.

 

Citation

GokulRaj  et al Bioinformation 10(6): 320-328 (2014)
 

Edited by

P Kangueane

 

ISSN

0973-2063

 

Publisher

Biomedical Informatics

 

License

This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.